This solution will contain spoilers! Be warned now! Tuuuuuurn away unless you don't care!
...are you still with me? Excellent!
The purpose of this guide is to help you acquire all 23 unique miracles in Dark Souls. Some can be bought, others found, and some are even awarded to you by completing certain tasks....
I will list every miracle and where it can be found. More in depth information will follow.01 (DROP - Duke's Archives) Bountiful Sunlight02 (DROP - Duke's Archives) Soothing Sunlight
These two miracles are very close to each other. In the Duke's Archives, you will be rudely transported to a large, tall room with a winding staircase. Simply get to the bottom of the room, and you will find a large jail cell with a whole lot of Pisacas guarding it (They look like seafood). As you clear this room out, you may notice the sound of women weeping softly. There are two Pisaca very near the cell that have their backs turned to you. Shuffle them off this mortal coil, and they "thank" you by dropping these miracles.
Don't feel bad about it. If I was transformed into that, I would want to die too :)03 (LOOT - Ash Lake) Reinforced Magic Barrier / Great Magic Barrier (Same thing, name may differ)
To find this one, make your way to Ash Lake. If you need help finding it, consult this guide:
Now that you are in Ash Lake, continue down the sand dunes until you reach another tree that you can enter (That is not the Great Hollows). Look for a root that curves around the tree on the outside and walk along it. Keep your eyes peeled for a ledge below your feet. Once you find it, carefully hop down and the miracle is at the end of the tunnel.04 (LOOT - Anor Londo) Sunlight Blade
This miracle can be found after defeating the covenant boss Gwyndolin
Be aware that should you engage Gwyndolin, you CANNOT access his covenant anymore. Farther down this guide I will go into detail as to why this is important.05 (LOOT - Catacombs) Tranquil Walk of Peace
This one is a bit tricky to find. Go through the catacombs until you activate the switch to flip the first spiked bridge. Cross it, and at the end you can roll off to the right side, landing on a patch of land right below. Follow this until you get to a ladder. Climb the ladder and you may find an NPC called Patches next to another switch.
If you let Patches live, he will try to kill you as you cross the bridge that switch activates. Just run across if you want him to live.
Once you get past all that, get to the bottom of this room, and you will see a rather crappy masonry job. Smash it with your weapon to reveal a dark room with 2 skeleton melee, and 2 skeleton archers. Clear that rubbish out and follow the corridor until you get to a necromancer. Kill him and look to your right. You will see a ladder in the wall. Climb up it to find a corpse with this miracle.
While you are in the area, the Darkmoon Seance ring is also found here, just before the necromancer. This is needed to join the Darkmoon covenant, which in turn is necessary for this achievement.06 (LOOT - Painted World of Ariamas) Vow of Silence
You must get the annex key in the painted world. It is underground with all the wheel skeletons. You will have to go through a few illusory walls, but keep looking and you'll find it with little trouble.
Once you have the key, make your way to the courtyard and head to the building ahead of you on the right side (assuming you are facing the direction of Priscilla). You will be in a church and a locked door is behind the pulpit. Go through, and once you finish climbing the stairs, take an immediate left and head up. You will climb another set of stairs being guarded by the world's biggest, angriest zit. Get past him and do watch for the giant hole in the roof. The miracle is being guarded by a total of four crows. Lure them to you; do NOT try to take on all four at once unless you are either insane or skilled.07 (COVENANT - Catacombs) Gravelord Sword Dance08 (COVENANT - Catacombs) Gravelord Greatsword Dance
I would advise against going for these two miracles until you have at least 11 eyes of death (You need 1 to access Nito's covenant). The frogs in the Depths drop them if you need to farm. In addition, the eyes are scattered about as loot around the world. You can also earn these through the PVP objectives within the covenant.
Here is how to find the Gravelord Covenant:
At rank 0, you are given the Gravelord Sword Miracle
At rank 1 (10 eyes of death), you are given the Gravelord Greatsword Miracle.09 (COVENANT - Anor Londo) Darkmoon Blade
Instead of killing Gwyndolin, you need to join his covenant and surrender 10 souvenir of reprisals. You can get 1 by avenging the fire keeper (Invade Lautrec's world and kill him), and 1 through trading the pendant to Sparkly (crow at Undead Asylum). You can farm these off of the crows in the Painted World as well. Remember where the miracle in the Painted World is? Excellent place to farm right there :) The drop rate is horrid, warning you now. You can also earn them by killing players in the book of sin (use the Darkmoon item to hunt a guilty player), but the drop rate isn't 100% there either.
At rank 1 (10 SoR), you get Darkmoon Blade.10 (COVENANT - Undead Parish) Lightning Spear11 (COVENANT - Undead Parish) Great Lightning Spear12 (COVENANT - Undead Parish) Sunlight Spear
This covenant is found at an altar on the other end of the bridge the red drake is guarding in the Undead Burg.
To join this covenant, you need to put a bit of commitment in. Either get your Faith to 25, or assist a player as a phantom in killing a boss. Each time you help kill a boss, your faith requirement is reduced by 5. Kill 2 bosses as a friendly phantom, and you only need 15 faith.
In addition, you will need 10 sunlight medals AND the soul of Gwyn the Firelord. You can earn the medals by summoning Solaire to help with various fights in the game (he must survive). You can also earn one by saving Lautrec from the prison cell in the Undead Parish. There's a chest by the 2nd bonfire in Anor Londo that has 3.
At rank 0, you get Lightning Spear
At rank 1 (10 medals) you get Great Lightning Spear
At rank 1 (Soul of Gwyn) you get Sunlight Spear13 (REWARD - Firelink Shrine) Emit Force
Find Seigmeyer of Catalina outside of Sen's Fortress before the doors open. Speak with him until all dialogue is exhausted.
When you go through Sen's Fortress later, Seigmeyer is outside near where you see your first boulder. Jump down to him, and listen to him lament about the boulders. Afterwards, change the boulder trap's direction to elsewhere (it's a large mechanism. Cannot miss it).
In Anor Londo, you will find Seigmeyer again. To reach him, go through the castle until you climb a small set of winding steps. You will be on a rooftop, and there will be a silver knight immediately in front of you. Kill him and go down the flight of steps he guards. Talk to Seigmeyer and listen to him cry about the silver knights in the next room. Clear the room out and talk to him again for a reward.
Head back to Firelink Shrine and talk to Seigmeyer by the bonfire. Answer "Yes" to his question. You will be given the miracle.14 (REWARD - Tomb of the Giants) Replenishment
All the following NPCs can be found at Firelink Shrine. Petrus is a rather large cleric who gives you the option to join Covenant of White. Rhea, Vance and Nico will appear by Petrus later in the story. Speak with all of them until all dialogue is exhausted. This will trigger them to leave when you do.
After Rhea, Vance, Nico and Petrus leave to go to the Catacombs, leave and come back a few times (throwing yourself off the cliff at Firelink works nicely) until Petrus returns. If you want to use Rhea as a shop later, I would strongly recommend killing Petrus AFTER he returns. If you kill him before Rhea is at Firelink, she and her two guards will go hostile.
The reason I say this is because Petrus really, REALLY hates Rhea. So much he will attempt to kill her if she ever leaves the tomb. That sucks. We don't want that to happen. Take no chances, and just kill him.
Of course, if you need miracles before hand, he will sell you a few... at much higher rates than Rhea does. He doesn't have them all though, so mentioning his inventory is redundant here.
You can find Rhea in Tomb of the Giants, in the pit that Patches throws you down. If you killed him, the pit is by the first bonfire in TotGiants. Climb the ladder and head left. If you look down you will see 3 souls. Rhea is down there along with her bodyguards. Once you kill her (hollowed) guards, talk to her and she thanks you by giving this miracle to you. 15 (PURCHASE 1000 - Rhea) Heal
16 (PURCHASE 10000 - Rhea) Great Heal
17 (PURCHASE 2000 - Rhea) Great Heal Excerpt
18 (PURCHASE 1000 - Rhea) Homeward
19 (PURCHASE 1000 - Rhea) Force
20 (PURCHASE 10000 - Rhea) Wrath of the Gods
21 (PURCHASE 500 - Rhea) Seek Guidance
22 (PURCHASE 6000 - Rhea) Magic Barrier
Once you have helped Rhea in Tomb of the Giants and have killed Nito, Rhea will leave for the undead parish. She will be praying at the same place you found your first Fire Keeper Soul.
If Petrus is still alive, warp from Nito's room to Firelink, then use the elevator shortcut to talk to her. Straying from seeing her right away usually ends in her dead otherwise (Thanks Petrus! You're the best!).
****Feb 29th Edit****
I myself have not confirmed this, but according to kungfucolin:
"To purchase the Miracles from Rhea, you don't need to kill Nito, you just need to have rescued her from the hollow clerics. I confirmed this not 5 minutes ago :)"
************************23 (PURCHASE 40000 - Oswald) Karmic Justice
This cocky looking guy can be found at the base of the of the first bell tower, past the gargoyle tag team. You must ring the first bell for him to appear.
Wow this was lengthy. Feedback, lemme know! I used the official guide for references here and there (Prices, Seigmeyer, making sure I got all the miracles, a couple of factions). The rest was run off of personal experience.
Edited for even more text, clarification, typos, and errors corrected. Nonsensical sentences stay however because I like cheese.